Comparison between the types for the ages and genders¶
Questions
- What are the differences between the type for the different combinations of ages and genders?
- Do we observe the same changes as globally?
Warning message in is.na(x[[i]]): “is.na() applied to non-(list or vector) of type 'environment'”Warning message in rsqlite_fetch(res@ptr, n = n): “Don't need to call dbFetch() for statements, only for queries”
========================================================================== * * Package WGCNA 1.63 loaded. * * Important note: It appears that your system supports multi-threading, * but it is not enabled within WGCNA in R. * To allow multi-threading within WGCNA with all available cores, use * * allowWGCNAThreads() * * within R. Use disableWGCNAThreads() to disable threading if necessary. * Alternatively, set the following environment variable on your system: * * ALLOW_WGCNA_THREADS=<number_of_processors> * * for example * * ALLOW_WGCNA_THREADS=4 * * To set the environment variable in linux bash shell, type * * export ALLOW_WGCNA_THREADS=4 * * before running R. Other operating systems or shells will * have a similar command to achieve the same aim. * ========================================================================== Allowing multi-threading with up to 4 threads. [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..."
Data¶
Stats¶
| Wald padj < 0.05 | LFC > 0 (Wald padj < 0.05) | LFC < 0 (Wald padj < 0.05) | |
|---|---|---|---|
| GF VS SPF (F, 8w) | 392 | 192 | 200 |
| GF VS SPF (M, 8w) | 161 | 76 | 85 |
| GF VS SPF (F, 52w) | 738 | 316 | 422 |
| GF VS SPF (M, 52w) | 393 | 145 | 248 |
| GF VS SPF (F, 104w) | 2038 | 846 | 1192 |
| GF VS SPF (M, 104w) | 2172 | 898 | 1274 |
Differentially expressed genes¶
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in stack.default(getgo(rownames(l$deg), "mm10", "geneSymbol")): “non-vector elements will be ignored”Warning message in stack.default(getgo(rownames(l$deg), "mm10", "geneSymbol", fetch.cats = "KEGG")): “non-vector elements will be ignored”
Comparison of the numbers per ages¶
Differentially expressed genes
DEG into gene co-expression network¶
- White: up-regulated
- Black: down-regulated
| GF vs SPF | 8w | 52w | 104w |
|---|---|---|---|
| F | |||
| M |
GO analysis¶
Biological process¶
Dot-plot with the most over-represented BP GO (20 most significant p-values for the different comparison)
Network based on description similarity
| GF vs SPF | 8w | 52w | 104w |
|---|---|---|---|
| F | |||
| M |
GF VS SPF (F, 8w)
<!DOCTYPE html>
GF VS SPF (M, 8w)
<!DOCTYPE html>
GF VS SPF (F, 52w)
<!DOCTYPE html>
GF VS SPF (M, 52w)
<!DOCTYPE html>
GF VS SPF (F, 104w)
<!DOCTYPE html>
GF VS SPF (M, 104w)
<!DOCTYPE html>
Cellular components¶
Dot-plot with the most over-represented CC GO (20 most significant p-values for the different comparison)
Warning message: “Removed 6 rows containing missing values (geom_point).”
Molecular functions¶
Dot-plot with the most over-represented MF GO (20 most significant p-values for the different comparison)
Warning message: “Removed 6 rows containing missing values (geom_point).”
KEGG pathways¶
[1] "Note: 39 of 3451 unique input IDs unmapped." [1] "Note: 39 of 3451 unique input IDs unmapped."
Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”
Pathway graphs available at ../results/dge/type-effect/type_gender_age/over_repr_kegg/
[1] "Note: 39 of 3451 unique input IDs unmapped."
Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"): “Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead.”
Pathway graphs available at ../results/dge/type-effect/type_gender_age/under_repr_kegg/
Comparison with Erny results¶
Protocol: 2 months old female mices (GF vs SPF)
Raw comparison of the results¶
| Symbols | Genes | fold.d.h | GF_1 | GF_2 | GF_3 | GF_4 | GF_5 | GF_7 | GF_8 | SPF_1 | SPF_2 | SPF_3 | SPF_4 | SPF_6 | SPF_7 | SPF_8 | t.test |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ddit4 | NM_029083 | 3.488386 | 232 | 420 | 140 | 116 | 1027 | 785 | 501 | 40 | 21 | 22 | 13 | 73 | 70 | 48 | 0.007198903 |
| Iqgap1 | NM_016721 | 2.545650 | 24 | 44 | 10 | 16 | 20 | 17 | 50 | 4 | 14 | 2 | 3 | 1 | 6 | 1 | 0.003764139 |
| Tsc22d3 | NM_001077364 | 2.416164 | 47 | 107 | 44 | 53 | 257 | 214 | 132 | 23 | 17 | 23 | 20 | 39 | 16 | 22 | 0.009737505 |
| Rab3d | NM_031874 | 2.369234 | 7 | 14 | 5 | 10 | 2 | 7 | 17 | 1 | 1 | 1 | 1 | 3 | 1 | 4 | 0.004171454 |
| Gnaz | NM_010311 | 2.280108 | 1 | 1 | 5 | 5 | 9 | 9 | 4 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0.009123198 |
| Agpat4 | NM_026644 | 1.984893 | 5 | 21 | 21 | 10 | 15 | 10 | 13 | 4 | 7 | 1 | 1 | 5 | 5 | 1 | 0.001279054 |
- 1700037C18Rik
- -0.726653411890693
- Lrmda
- -3.64638532054075
- Tcim
- 1.05252272836875
- Ccdc191
- -1.07325728126671
- 2610524H06Rik
- 1.32511199395419
- 6330407A03Rik
- -1.99177874144356
| erny | our | |
|---|---|---|
| Ddit4 | 3.4883860 | 3.6294025 |
| Tsc22d3 | 2.4161642 | 1.4193018 |
| Notch4 | 1.4226911 | 1.6315226 |
| Sult1a1 | 1.2561528 | 1.1617315 |
| Capg | 0.9126729 | 0.5168264 |
| Ucp2 | 0.9111967 | 0.5044607 |
| Gpr137b | 0.8032544 | 1.2266600 |
| Pnpla2 | 0.7100179 | 0.4259134 |
| Ogfrl1 | 0.6877922 | 0.6959325 |
| Arhgef6 | -1.0246621 | 0.4253851 |
| Gpr137b-ps | -1.1178365 | -3.0251734 |
| Upk1b | -1.1300605 | -0.6517569 |
| Cntrl | -1.3303078 | -0.9347969 |
| Apobec2 | -1.4288433 | -0.8472098 |
| Ly86 | -1.4389640 | -0.9562232 |
| Stard3nl | -1.4780473 | -0.4310033 |
| Fkbp7 | -1.6261852 | -0.3942576 |
| Malat1 | -1.7120031 | -1.1023659 |
| Mcur1 | -1.7424200 | -0.8593199 |
| Nos1ap | -1.8022360 | -0.8171791 |
| Zfp318 | -1.8961642 | -0.7895965 |
| Lrba | -2.0198996 | -0.6372855 |
| Far1 | -2.5766472 | 0.5588240 |
| Ero1lb | -3.2172307 | -1.3952799 |
Detailed comparison¶
- Checking the correlation between the counts of Erny and our counts
- Re-running a DGE analysis on the Erny's raw counts
Error in counts[, SPF_F_8w_samples]: object of type 'closure' is not subsettable Traceback: